Updates about NMR structures

help.md

@@ -56,16 +56,16 @@ Once you specify the nucleotides of interest from a particular structure, R3DMCS
 R3DMCS uses the Equivalence Classes in the [BGSU RNA Representative Sets](http://rna.bgsu.edu/rna3dhub/nrlist) to identify the 3D structures of the same molecule from the same organism.  For example, the [E. coli SSU equivalence class NR_3.0_56726.129](http://rna.bgsu.edu/rna3dhub/nrlist/view/NR_3.0_56726.129) collects all 166 small subunit ribosomal RNA chains from different 3D structures solved at 3.0Å or better resolution, as of October 15, 2024.  Sequence-based alignments between these chains are computed each week for newly added chains, and R3DMCS uses those alignments to find corresponding nucleotides.
 
 #### Homologous nucleotides from the same molecule in different organisms
-R3DMCS uses multiple sequence alignments produced by the BGSU RNA pipeline using [Infernal](http://eddylab.org/infernal/) and based on [Rfam covariance models](https://docs.rfam.org/en/latest/glossary.html#:~:text=Clustal%20web%20server.-,Covariance%20model%20(CM),in%20RNA%20or%20DNA%20sequences.), for all PDB chain sequences in each Rfam family.  The Rfam covariance models are downloaded with each Rfam release.  Infernal and the covariance models are used each week to map PDB chains to Rfam families.  For example, the E. coli SSU chain AA from PDB structure 5J7L maps to Rfam family RF00177.  To see all of the other chains that map to Rfam family RF00177, one can go to a [Representative Set release page](http://rna.bgsu.edu/rna3dhub/nrlist/release/3.332/3.0A) and type RF00177 in the Filter box.  As of the April 24, 2024 release at 3.0Å resolution threshold, this results in 21 equivalence classes.  Of these, 15 correspond to bacterial species, 5 to mitochondrial ribosomes, and 1 to a chloroplast ribosome.  The number of chains in each equivalence class varies from 1 to 206.  To avoid over-representation from any one equivalence class, the following input parameter can be used when retrieving over different organisms:
+R3DMCS uses multiple sequence alignments produced by the BGSU RNA pipeline using [Infernal](http://eddylab.org/infernal/) and based on [Rfam covariance models](https://docs.rfam.org/en/latest/glossary.html#:~:text=Clustal%20web%20server.-,Covariance%20model%20(CM),in%20RNA%20or%20DNA%20sequences.), for all PDB chain sequences in each Rfam family.  The Rfam covariance models are downloaded with each Rfam release.  Infernal and the covariance models are used each week to map PDB chains to Rfam families.  For example, the E. coli SSU chain AA from PDB structure 5J7L maps to Rfam family RF00177.  To see all of the other chains that map to Rfam family RF00177, one can go to a [Representative Set release page](http://rna.bgsu.edu/rna3dhub/nrlist/release/current/3.0A) and type RF00177 in the Filter box.  As of the October 9, 2024 release at 3.0Å resolution threshold, this results in 21 equivalence classes.  Of these, 15 correspond to bacterial species, 5 to mitochondrial ribosomes, and 1 to a chloroplast ribosome.  The number of chains in each equivalence class varies from 1 to 228.  To avoid over-representation from any one equivalence class, the following input parameter can be used when retrieving over different organisms:
 
 ##### Depth
-This parameter tells the maximum number of chains in each equivalence class to use for the retrieval across different organisms.  The chains are prioritized in the order that they are listed on the Representative Set page, which is according to six structure quality factors, which are briefly described on the [Representative Set home page](http://rna.bgsu.edu/rna3dhub/nrlist).
+The depth parameter tells the maximum number of chains in each equivalence class to use for the retrieval across different organisms.  The chains are prioritized in the order that they are listed on the Representative Set page, which is according to six structure quality factors, which are briefly described on the [Representative Set home page](http://rna.bgsu.edu/rna3dhub/nrlist).
 
 ### Step 3 - Resolution threshold
-The BGSU RNA site organizes equivalence classes (chains of the same molecule from the same species) by resolution, keeping all structures solved up to a threshold value.  Setting the resolution threshold makes it possible to look only at the highest resolution structures.  The query will retrieve corresponding motif instances from all chains in the equivalence class with resolution up to the resolution threshold.  The default resolution threshold is 3 Ångstroms.  Note that NMR structures have no reported resolution, and can only be retrieved by setting the resolution threshold to "all".
+The BGSU RNA site organizes equivalence classes (chains of the same molecule from the same species) by resolution, keeping all structures solved up to a threshold value.  Setting the resolution threshold makes it possible to look only at the highest resolution structures.  The query will retrieve corresponding motif instances from all chains in the equivalence class with resolution up to the resolution threshold.  The default resolution threshold is 3 Ångstroms.  Note that NMR structures have no reported resolution, and can be retrieved only by setting the resolution threshold to "all".
 
 ### Step 4 - Experimental technique
-Choose the desired experimental technique. Users can choose X-ray diffraction, cryo-EM microscopy, or “all” which also includes NMR and other techniques besides X-ray and cryo-EM.
+Choose the desired experimental technique. Users can choose X-ray diffraction, cryo-EM microscopy, NMR, or “all” which includes all techniques above.
 
 ### Step 5 - PDB identifiers to exclude
 Occasionally a PDB entry will have a very different 3D structure in a specific region, due to a variety of factors such as the presence of a modified nucleotide, a bound ligand, or a modeling feature that sets it far apart from other structures.  If it is desired to exclude those instances in order to focus on ones of more direct interest, it is possible to give a list of PDB identifiers to exclude.  For example, in the [example of individual residue numbers](http://rna.bgsu.edu/correspondence/comparison?selection=1405,1496&pdb=5J7L&chain=AA&exp_method=all&resolution=3.0&scope=EC&input_form=True) from above, the structures 4V9O and 4V9P model C1496 in syn, which sets them apart from the other instances.  Also, structure 8GHU has the non-standard residue ZIV at position 1405, which has two bases in one nucleotide and so is not compared geometrically to the other instances, which is shown with gray cells in the heat map.  [Listing these three structures under PDB identifiers to exclude](http://rna.bgsu.edu/correspondence/comparison?selection=1405,1496&pdb=5J7L&chain=AA&exp_method=all&resolution=3.0&scope=EC&exclude=4V9O,4V9P,8GHU&input_form=True) removes these instances, and the heat map coloring adjusts accordingly, making it easier to see the high degree of similarity between the remaining instances.
@@ -258,4 +258,5 @@ R3DMCS can retrieve hundreds of instances, but the all-against-all geometric com
 ### No discrepancy calculated when an instance is missing atoms
 Some 3D structures have nucleotides with missing atoms, for example, missing base atoms.  As of April 2024, no discrepancy is calculated with those instances, but the nucleotides are shown in the table and in the heat map.
 
-
+### Partial alignments
+In some cases, only some of the query nucleotides can be aligned to nucleotides in another structure, which is called a partial alignment.  Partial alignments are not returned by R3DMCS.  In some cases, only partial alignments are found, and R3DMCS reports that the query returned no results.